BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 032554
(138 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Y1R|A Chain A, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|B Chain B, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|C Chain C, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|D Chain D, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|E Chain E, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|F Chain F, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|G Chain G, Structure Of Meca121 & Clpc N-Domain Complex
pdb|2Y1R|H Chain H, Structure Of Meca121 & Clpc N-Domain Complex
Length = 149
Score = 63.9 bits (154), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 41/120 (34%), Positives = 66/120 (55%), Gaps = 4/120 (3%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPE 64
EA +L H GTE IL+G++ EG +AAK L A G+ K++ E ++G+G +
Sbjct: 20 EALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEMSQTIH 79
Query: 65 HPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAK 124
+ P A++VI+ ++D K G+S V +LLG+ E + ++L LG S KA+
Sbjct: 80 YTP---RAKKVIELSMDEARKLGHS-YVGTEHILLGLIREGEGVAARVLNNLGVSLNKAR 135
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGD 57
EARKL H GTE IL+G++ EG +AA+ L GV+L K R + ++++G +
Sbjct: 94 EARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSNE 146
>pdb|2K77|A Chain A, Nmr Solution Structure Of The Bacillus Subtilis Clpc N-
Domain
Length = 146
Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 41/120 (34%), Positives = 66/120 (55%), Gaps = 4/120 (3%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPE 64
EA +L H GTE IL+G++ EG +AAK L A G+ K++ E ++G+G +
Sbjct: 21 EALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEMSQTIH 80
Query: 65 HPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAK 124
+ P A++VI+ ++D K G+S V +LLG+ E + ++L LG S KA+
Sbjct: 81 YTP---RAKKVIELSMDEARKLGHS-YVGTEHILLGLIREGEGVAARVLNNLGVSLNKAR 136
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 34/50 (68%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVG 54
EARKL H GTE IL+G++ EG +AA+ L GV+L K R + ++++G
Sbjct: 95 EARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLG 144
>pdb|3FH2|A Chain A, The Crystal Structure Of The Probable Atp-Dependent
Protease (Heat Shock Protein) From Corynebacterium
Glutamicum
Length = 146
Score = 63.2 bits (152), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 41/115 (35%), Positives = 64/115 (55%), Gaps = 7/115 (6%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPE 64
EAR L H GTE IL+G++ EG +AAK L + G++L VR E +I+G+G P
Sbjct: 21 EARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDAVRQEVEEIIGQGS----QPT 76
Query: 65 --HPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALG 117
H P T A++V++ ++ L+ G+ + LLLG+ E + ++L LG
Sbjct: 77 TGHIPFTPRAKKVLELSLREGLQMGHK-YIGTEFLLLGLIREGEGVAAQVLVKLG 130
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIV 53
E ++ H GTE +L+G++ EG +AA+ L G L +VR + ++++
Sbjct: 96 EGLQMGHKYIGTEFLLLGLIREGEGVAAQVLVKLGADLPRVRQQVIQLL 144
>pdb|3PXI|A Chain A, Structure Of Meca108:clpc
pdb|3PXI|B Chain B, Structure Of Meca108:clpc
pdb|3PXI|C Chain C, Structure Of Meca108:clpc
Length = 758
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 41/124 (33%), Positives = 68/124 (54%), Gaps = 4/124 (3%)
Query: 1 MGELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFF 60
+ + EA +L H GTE IL+G++ EG +AAK L A G+ K++ E ++G+G
Sbjct: 16 LAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEMS 75
Query: 61 FSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSD 120
+ + P A++VI+ ++D K G+S V +LLG+ E + ++L LG S
Sbjct: 76 QTIHYTP---RAKKVIELSMDEARKLGHSY-VGTEHILLGLIREGEGVAARVLNNLGVSL 131
Query: 121 EKAK 124
KA+
Sbjct: 132 NKAR 135
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGD 57
EARKL H GTE IL+G++ EG +AA+ L GV+L K R + ++++G +
Sbjct: 94 EARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSNE 146
>pdb|2Y1Q|A Chain A, Crystal Structure Of Clpc N-Terminal Domain
Length = 150
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/120 (33%), Positives = 65/120 (54%), Gaps = 4/120 (3%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPE 64
EA +L H GTE IL+G++ EG +AAK L A G+ K++ E ++G+ +
Sbjct: 20 EALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRAQEMSQTIH 79
Query: 65 HPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAK 124
+ P A++VI+ ++D K G+S V +LLG+ E + ++L LG S KA+
Sbjct: 80 YTP---RAKKVIELSMDEARKLGHS-YVGTEHILLGLIREGEGVAARVLNNLGVSLNKAR 135
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGD 57
EARKL H GTE IL+G++ EG +AA+ L GV+L K R + ++++G +
Sbjct: 94 EARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGNNE 146
>pdb|3PXG|A Chain A, Structure Of Meca121 And Clpc1-485 Complex
pdb|3PXG|B Chain B, Structure Of Meca121 And Clpc1-485 Complex
pdb|3PXG|C Chain C, Structure Of Meca121 And Clpc1-485 Complex
pdb|3PXG|D Chain D, Structure Of Meca121 And Clpc1-485 Complex
pdb|3PXG|E Chain E, Structure Of Meca121 And Clpc1-485 Complex
pdb|3PXG|F Chain F, Structure Of Meca121 And Clpc1-485 Complex
Length = 468
Score = 58.5 bits (140), Expect = 1e-09, Method: Composition-based stats.
Identities = 41/124 (33%), Positives = 68/124 (54%), Gaps = 4/124 (3%)
Query: 1 MGELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFF 60
+ + EA +L H GTE IL+G++ EG +AAK L A G+ K++ E ++G+G
Sbjct: 16 LAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEMS 75
Query: 61 FSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSD 120
+ + P A++VI+ ++D K G+S V +LLG+ E + ++L LG S
Sbjct: 76 QTIHYTP---RAKKVIELSMDEARKLGHS-YVGTEHILLGLIREGEGVAARVLNNLGVSL 131
Query: 121 EKAK 124
KA+
Sbjct: 132 NKAR 135
Score = 45.8 bits (107), Expect = 7e-06, Method: Composition-based stats.
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 5 EARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGD 57
EARKL H GTE IL+G++ EG +AA+ L GV+L K R + ++++G +
Sbjct: 94 EARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSNE 146
>pdb|3FES|A Chain A, Crystal Structure Of The Atp-Dependent Clp Protease Clpc
From Clostridium Difficile
pdb|3FES|B Chain B, Crystal Structure Of The Atp-Dependent Clp Protease Clpc
From Clostridium Difficile
pdb|3FES|C Chain C, Crystal Structure Of The Atp-Dependent Clp Protease Clpc
From Clostridium Difficile
pdb|3FES|D Chain D, Crystal Structure Of The Atp-Dependent Clp Protease Clpc
From Clostridium Difficile
Length = 145
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 57/117 (48%), Gaps = 8/117 (6%)
Query: 6 ARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEH 65
A+ L H G+E IL+G+L E +AAK L G T + + V GKG+ E
Sbjct: 23 AKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDXEGKGEEI---SED 79
Query: 66 PPLTEDAQRVIDWA--VDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSD 120
L+ ++++++ + +KLK+ G +LL I E + +KIL G +D
Sbjct: 80 IVLSPRSKQILELSGXFANKLKTNYIG---TEHILLAIIQEGEGIANKILNYAGVND 133
>pdb|3A4X|A Chain A, Crystal Structures Of Catalytic Site Mutants Of Active
Domain 2 Of Thermostable Chitinase From Pyrococcus
Furiosus Complexed With Chito- Oligosaccharides
pdb|3A4X|B Chain B, Crystal Structures Of Catalytic Site Mutants Of Active
Domain 2 Of Thermostable Chitinase From Pyrococcus
Furiosus Complexed With Chito- Oligosaccharides
pdb|3AFB|A Chain A, Crystal Structures Of Catalytic Site Mutants Of Active
Domain 2 Of Chitinase From Pyrococcus Furiosus
pdb|3AFB|B Chain B, Crystal Structures Of Catalytic Site Mutants Of Active
Domain 2 Of Chitinase From Pyrococcus Furiosus
Length = 311
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 13/41 (31%)
Query: 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS-ETDSPG 109
EDAQ+++DWA+ HK+ S L WS + D PG
Sbjct: 238 EDAQQLVDWAIQHKIGS------------LAFWSVDRDHPG 266
>pdb|2DSK|A Chain A, Crystal Structure Of Catalytic Domain Of Hyperthermophilic
Chitinase From Pyrococcus Furiosus
pdb|2DSK|B Chain B, Crystal Structure Of Catalytic Domain Of Hyperthermophilic
Chitinase From Pyrococcus Furiosus
Length = 311
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 13/41 (31%)
Query: 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS-ETDSPG 109
EDAQ+++DWA+ HK+ S L WS + D PG
Sbjct: 238 EDAQQLVDWAIQHKIGS------------LAFWSVDRDHPG 266
>pdb|3A4W|A Chain A, Crystal Structures Of Catalytic Site Mutants Of Active
Domain 2 Of Thermostable Chitinase From Pyrococcus
Furiosus Complexed With Chito- Oligosaccharides
pdb|3A4W|B Chain B, Crystal Structures Of Catalytic Site Mutants Of Active
Domain 2 Of Thermostable Chitinase From Pyrococcus
Furiosus Complexed With Chito- Oligosaccharides
Length = 311
Score = 30.4 bits (67), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 13/41 (31%)
Query: 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS-ETDSPG 109
EDAQ+++DWA+ HK+ S L WS + D PG
Sbjct: 238 EDAQQLVDWAIQHKIGS------------LAFWSVDRDHPG 266
>pdb|1IQD|A Chain A, Human Factor Viii C2 Domain Complexed To Human Monoclonal
Bo2c11 Fab
Length = 211
Score = 29.3 bits (64), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 34/111 (30%), Positives = 48/111 (43%), Gaps = 18/111 (16%)
Query: 15 GTEAILMGILVEGTSLAAK-FLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQ 73
GT AI G +GT L K + A V +F DE +K + +P +A+
Sbjct: 92 GTSAITFG---QGTRLEIKGTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYP---REAK 145
Query: 74 RVIDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 --VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|3M8O|L Chain L, Human Iga1 Fab Fragment
pdb|3QNX|A Chain A, Orthorhombic Form Of Human Iga1 Fab Fragment, Sharing Same
Fv As Igg
pdb|3QNY|A Chain A, Monoclinic Form Of Human Iga1 Fab Fragment, Sharing Same
Fv As Igg
pdb|3QNY|C Chain C, Monoclinic Form Of Human Iga1 Fab Fragment, Sharing Same
Fv As Igg
pdb|3QNZ|A Chain A, Orthorhombic Form Of Igg1 Fab Fragment (in Complex With
Antigenic Tubulin Peptide) Sharing Same Fv As Iga
pdb|3QO0|A Chain A, Monoclinic Form Of Igg1 Fab Fragment (In Complex With
Antigenic Peptide) Sharing Same Fv As Iga
pdb|3QO1|A Chain A, Monoclinic Form Of Igg1 Fab Fragment (apo Form) Sharing
Same Fv As Iga
Length = 219
Score = 28.9 bits (63), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 43/128 (33%), Gaps = 26/128 (20%)
Query: 14 TGTEAILMGILVEGTSLAAKFLWANGVTLFK----VRDESVKIVGKGDFFFFSPEHPPLT 69
+GT+ L I VE + N T R E + V F F P L
Sbjct: 72 SGTDFTLKIIRVEAEDAGTYYCMQNKQTPLTFGQGTRLEIKRTVAAPSVFIFPPSDEQLK 131
Query: 70 EDAQRVI-------------DWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDS 107
V+ W VD+ L+SGNS E VT D + S+ D
Sbjct: 132 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 191
Query: 108 PGHKILAA 115
HK+ A
Sbjct: 192 EKHKVYAC 199
>pdb|1HZH|L Chain L, Crystal Structure Of The Intact Human Igg B12 With Broad
And Potent Activity Against Primary Hiv-1 Isolates: A
Template For Hiv Vaccine Design
pdb|1HZH|M Chain M, Crystal Structure Of The Intact Human Igg B12 With Broad
And Potent Activity Against Primary Hiv-1 Isolates: A
Template For Hiv Vaccine Design
pdb|1N0X|L Chain L, Crystal Structure Of A Broadly Neutralizing Anti-Hiv-1
Antibody In Complex With A Peptide Mimotope
pdb|1N0X|M Chain M, Crystal Structure Of A Broadly Neutralizing Anti-Hiv-1
Antibody In Complex With A Peptide Mimotope
pdb|2NY7|L Chain L, Hiv-1 Gp120 Envelope Glycoprotein Complexed With The
Broadly Neutralizing Cd4-Binding-Site Antibody B12
pdb|3RU8|L Chain L, Structure Of An Hiv Epitope Scaffold In Complex With
Neutralizing Antibody B12 Fab
Length = 215
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 44/128 (34%), Gaps = 26/128 (20%)
Query: 14 TGTEAILMGILVEGTSLAAKFLWANGVTLFK----VRDESVKIVGKGDFFFFSPEHPPLT 69
+GT+ L VE A + G + + + E + V F F P L
Sbjct: 68 SGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFPPSDEQLK 127
Query: 70 EDAQRVI-------------DWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDS 107
V+ W VD+ L+SGNS E VT D + S+ D
Sbjct: 128 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 187
Query: 108 PGHKILAA 115
HK+ A
Sbjct: 188 EKHKVYAC 195
>pdb|2VXQ|L Chain L, Crystal Structure Of The Major Grass Pollen Allergen Phl P
2 In Complex With Its Specific Ige-Fab
Length = 214
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 39/109 (35%), Gaps = 27/109 (24%)
Query: 29 SLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVI------------ 76
SL+A + + G + E + V F F P L V+
Sbjct: 91 SLSASYTFGQGTKV-----EIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK 145
Query: 77 -DWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|1U6A|L Chain L, Crystal Structure Of The Broadly Neutralizing Anti-Hiv Fab
F105
pdb|3HI1|L Chain L, Structure Of Hiv-1 Gp120 (Core With V3) In Complex With
Cd4-Binding- Site Antibody F105
pdb|3HI1|A Chain A, Structure Of Hiv-1 Gp120 (Core With V3) In Complex With
Cd4-Binding- Site Antibody F105
Length = 215
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 45/128 (35%), Gaps = 26/128 (20%)
Query: 14 TGTEAILMGILVEGTSLAAKFL--WANGVTLFK--VRDESVKIVGKGDFFFFSPEHPPLT 69
+GT+ L VE A + + N V F + E + V F F P L
Sbjct: 68 SGTDFTLTISRVEPEDFAVYYCQQYDNSVCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLK 127
Query: 70 EDAQRVI-------------DWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDS 107
V+ W VD+ L+SGNS E VT D + S+ D
Sbjct: 128 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 187
Query: 108 PGHKILAA 115
HK+ A
Sbjct: 188 EKHKVYAC 195
>pdb|3MEM|A Chain A, Crystal Structure Of A Putative Signal Transduction
Protein (Maqu_0641) From Marinobacter Aquaeolei Vt8 At
2.25 A Resolution
Length = 457
Score = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 64 EHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASD 96
E PPL E AQR+I V+ G+ +V SD
Sbjct: 183 ELPPLPETAQRIIHLRVNPNAVXGDLVDVVESD 215
>pdb|3RPI|L Chain L, Crystal Structure Of Fab From 3bnc60, Highly Potent
Anti-Hiv Antibody
pdb|3RPI|B Chain B, Crystal Structure Of Fab From 3bnc60, Highly Potent
Anti-Hiv Antibody
Length = 206
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 138 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 186
>pdb|3I9G|L Chain L, Crystal Structure Of The Lt1009 (Sonepcizumab) Antibody
Fab Fragment In Complex With Sphingosine-1-Phosphate
Length = 213
Score = 26.6 bits (57), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|1RHH|A Chain A, Crystal Structure Of The Broadly Hiv-1 Neutralizing Fab X5
At 1.90 Angstrom Resolution
pdb|1RHH|C Chain C, Crystal Structure Of The Broadly Hiv-1 Neutralizing Fab X5
At 1.90 Angstrom Resolution
pdb|2B4C|L Chain L, Crystal Structure Of Hiv-1 Jr-fl Gp120 Core Protein
Containing The Third Variable Region (v3) Complexed With
Cd4 And The X5 Antibody
Length = 215
Score = 26.6 bits (57), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASD-----LLLG---IWSETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D LG S+ D HK+ A
Sbjct: 147 VQWKVDNALQSGNSQESVTEQDSRDSTYSLGSTLTLSKADYEKHKVYAC 195
>pdb|1IT9|L Chain L, Crystal Structure Of An Antigen-Binding Fragment From A
Humanized Version Of The Anti-Human Fas Antibody Hfe7a
Length = 214
Score = 26.6 bits (57), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 150 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 198
>pdb|1RZI|A Chain A, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|C Chain C, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|E Chain E, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|G Chain G, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|I Chain I, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|K Chain K, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|M Chain M, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
pdb|1RZI|O Chain O, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 47e Fab
Length = 212
Score = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 145 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 193
>pdb|3SO3|B Chain B, Structures Of Fab-Protease Complexes Reveal A Highly
Specific Non- Canonical Mechanism Of Inhibition
Length = 217
Score = 26.6 bits (57), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 36/103 (34%), Gaps = 23/103 (22%)
Query: 36 WANGVTLFK-VRDESVKIVGKGDFFFFSPEHPPLTEDAQRVI-------------DWAVD 81
W G T + + E + V F F P L V+ W VD
Sbjct: 95 WPPGYTFGQGTKVEITRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVD 154
Query: 82 HKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 155 NALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 197
>pdb|3L5X|L Chain L, Crystal Structure Of The Complex Between Il-13 And H2l6
Fab
pdb|3L7F|L Chain L, Structure Of Il-13 Antibody H2l6, A Humanized Variant Of
C836
pdb|3L7F|A Chain A, Structure Of Il-13 Antibody H2l6, A Humanized Variant Of
C836
pdb|3L7F|D Chain D, Structure Of Il-13 Antibody H2l6, A Humanized Variant Of
C836
Length = 214
Score = 26.6 bits (57), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|3L5Y|L Chain L, Crystal Structure Of The Complex Between Il-13 And M1295
Fab
Length = 213
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 145 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 193
>pdb|3HMW|L Chain L, Crystal Structure Of Ustekinumab Fab
pdb|3HMX|L Chain L, Crystal Structure Of Ustekinumab FabIL-12 Complex
Length = 214
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|3SQO|L Chain L, Pcsk9 J16 Fab Complex
Length = 214
Score = 26.2 bits (56), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|2X7L|L Chain L, Implications Of The Hiv-1 Rev Dimer Structure At 3.2a
Resolution For Multimeric Binding To The Rev Response
Element
pdb|2X7L|B Chain B, Implications Of The Hiv-1 Rev Dimer Structure At 3.2a
Resolution For Multimeric Binding To The Rev Response
Element
pdb|2X7L|D Chain D, Implications Of The Hiv-1 Rev Dimer Structure At 3.2a
Resolution For Multimeric Binding To The Rev Response
Element
pdb|2X7L|K Chain K, Implications Of The Hiv-1 Rev Dimer Structure At 3.2a
Resolution For Multimeric Binding To The Rev Response
Element
pdb|2X7L|F Chain F, Implications Of The Hiv-1 Rev Dimer Structure At 3.2a
Resolution For Multimeric Binding To The Rev Response
Element
pdb|2X7L|I Chain I, Implications Of The Hiv-1 Rev Dimer Structure At 3.2a
Resolution For Multimeric Binding To The Rev Response
Element
Length = 217
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 32/90 (35%), Gaps = 22/90 (24%)
Query: 48 ESVKIVGKGDFFFFSPEHPPLTEDAQRVI-------------DWAVDHKLKSGNSGE-VT 93
E ++ V F F P L V+ W VD+ L+SGNS E VT
Sbjct: 108 EIIRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVT 167
Query: 94 ASDLLLGIW--------SETDSPGHKILAA 115
D + S+ D HK+ A
Sbjct: 168 EQDSKDSTYSLSSTLTLSKADYEKHKVYAC 197
>pdb|4G6M|L Chain L, Crystal Strucure Of Human Il-1beta In Complex With
Therapeutic Antibody Binding Fragment Of Gevokizumab
Length = 213
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|3AAZ|B Chain B, Crystal Structure Of The Humanized Recombinant Fab
Fragment Of A Murine; Antibody
pdb|3AAZ|L Chain L, Crystal Structure Of The Humanized Recombinant Fab
Fragment Of A Murine; Antibody
Length = 229
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 151 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 199
>pdb|4G6K|L Chain L, Crystal Structure Of The Therapeutic Antibody Binding
Fragment Of Gevokizumab In Its Unbound State
Length = 212
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|2R56|L Chain L, Crystal Structure Of A Recombinant Ige Fab Fragment In
Complex With Bovine Beta-Lactoglobulin Allergen
pdb|2R56|M Chain M, Crystal Structure Of A Recombinant Ige Fab Fragment In
Complex With Bovine Beta-Lactoglobulin Allergen
Length = 211
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
>pdb|3EYF|A Chain A, Crystal Structure Of Anti-Human Cytomegalovirus Antibody
8f9 Plus Gb Peptide
pdb|3EYF|C Chain C, Crystal Structure Of Anti-Human Cytomegalovirus Antibody
8f9 Plus Gb Peptide
pdb|3EYO|A Chain A, Crystal Structure Of Anti-Human Cytomegalovirus Antibody
8f9
pdb|3EYO|C Chain C, Crystal Structure Of Anti-Human Cytomegalovirus Antibody
8f9
Length = 216
Score = 26.2 bits (56), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 148 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 196
>pdb|3QCT|L Chain L, Crystal Structure Of The Humanized Apo Lt3015
Anti-Lysophosphatidic Acid Antibody Fab Fragment
pdb|3QCU|L Chain L, Crystal Structure Of The Lt3015 Antibody Fab Fragment In
Complex With Lysophosphatidic Acid (14:0)
pdb|3QCU|M Chain M, Crystal Structure Of The Lt3015 Antibody Fab Fragment In
Complex With Lysophosphatidic Acid (14:0)
pdb|3QCV|L Chain L, Crystal Structure Of The Lt3015 Antibody Fab Fragment In
Complex With Lysophosphatidic Acid (18:2)
pdb|3QCV|M Chain M, Crystal Structure Of The Lt3015 Antibody Fab Fragment In
Complex With Lysophosphatidic Acid (18:2)
Length = 218
Score = 25.8 bits (55), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 151 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 199
>pdb|3BH6|B Chain B, Crystal Structure Of The Rp2-Arl3 Complex Bound To Gppnhp
pdb|3BH7|B Chain B, Crystal Structure Of The Rp2-Arl3 Complex Bound To
Gdp-Alf4
Length = 352
Score = 25.8 bits (55), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 26/60 (43%)
Query: 35 LWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTA 94
L+A T+ R ++VGKG F + E EDAQRV L N G V A
Sbjct: 242 LFAGDYTIANARKLIDEMVGKGFFLVQTKEVSMKAEDAQRVFREKAPDFLPLLNKGPVIA 301
>pdb|2BX6|A Chain A, Crystal Structure Of The Human Retinitis Pigmentosa
Protein 2 (Rp2)
Length = 350
Score = 25.8 bits (55), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 26/60 (43%)
Query: 35 LWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTA 94
L+A T+ R ++VGKG F + E EDAQRV L N G V A
Sbjct: 240 LFAGDYTIANARKLIDEMVGKGFFLVQTKEVSMKAEDAQRVFREKAPDFLPLLNKGPVIA 299
>pdb|1RZG|B Chain B, Crystal Structure Of Human Anti-hiv-1 Gp120 Reactive
Antibody 412d
pdb|1RZG|D Chain D, Crystal Structure Of Human Anti-hiv-1 Gp120 Reactive
Antibody 412d
pdb|2QAD|C Chain C, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
With Hiv-1 Yu2 Gp120 And Cd4
pdb|2QAD|G Chain G, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
With Hiv-1 Yu2 Gp120 And Cd4
Length = 214
Score = 25.8 bits (55), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 76 IDWAVDHKLKSGNSGE-VTASDLLLGIW--------SETDSPGHKILAA 115
+ W VD+ L+SGNS E VT D + S+ D HK+ A
Sbjct: 146 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYAC 194
>pdb|3IB3|A Chain A, Crystal Structure Of Sacol2612 - CoceNOND FAMILY HYDROLASE
FROM Staphylococcus Aureus
pdb|3IB3|B Chain B, Crystal Structure Of Sacol2612 - CoceNOND FAMILY HYDROLASE
FROM Staphylococcus Aureus
pdb|3III|A Chain A, 1.95 Angstrom Crystal Structure Of Coce/nond Family
Hydrolase (sacol2612) From Staphylococcus Aureus
Length = 560
Score = 25.4 bits (54), Expect = 9.6, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 61 FSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIW 102
SP ED VI+WA + +GN G S L + W
Sbjct: 135 LSPWSKREAEDYYEVIEWAANQSWSNGNIGTNGVSYLAVTQW 176
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.135 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,206,147
Number of Sequences: 62578
Number of extensions: 165281
Number of successful extensions: 422
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 394
Number of HSP's gapped (non-prelim): 45
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)